Once the spectrum image (SI) acquisition parameters and any artifact corrections are set up, select the Capture button on the SI palette to start an acquisition. If you wish to update the survey image before proceeding with acquisition, right-click on it and select Restart scan from the context menu.

Once started, the SI acquisition routine will take control of the microscope beam, and the acquisition then begins. During acquisition, the Capture button pulses in blue to indicate that an acquisition is active and that a subsequent click of the Capture button halts acquisition. A new workspace is created and filled with a copy of the survey image and data containers for all acquired signals.

Note: During active SI acquisition, the spectrometers in use are not available for single spectrum acquisition.

If spatial drift correction is enabled, then some preliminary measurements are performed. Visual feedback on the measurements may be provided, depending on the preferences specified.

You can monitor how the acquisition is proceeding using the visual feedback provided. Each SI displays in a new image window, which fills as the acquisition proceeds. Live spectra may also be shown or hidden as desired. If you wish to halt the acquisition, click on the pulsing Capture button. When the acquisition is halted or completes, the beam control returns to the Beam Safe Point (if one has been set up), or alternatively, it is returned to the microscope.


During a SI acquisition, it may become necessary to perform a microscope adjustment that temporarily degrades the data collected by the spectrometer. At such times, you should pause the acquisition, carry out the adjustment, and resume after conditions have stabilized. To pause the acquisition at any time, click on the pulsing Capture button in the STEM-SI palette while keeping the Alt key pressed at the same time—the label of the Capture button changes to Resume.

When you pause the acquisition, the beam either moves to the Beam Safe Point (if you defined one) or returns otherwise beam control to the microscope. If the acquisition is paused and restarted, the software immediately carries out spatial drift corrections if you enable Apply on Resume from Pause, before continuing to acquire data from where it was before the pause.

To resume acquisition from the paused state, click the Resume button. To stop acquisition from the paused state, click on the Resume button while pressing the Alt key at the same time.

Note: Pausing is not available for hardware synchronized acquisitions. On systems which by default use hardware synchronized acquisition, you can force software synchronization via the Setup dialog.

After the acquisition

If the autosave functionality is enabled, all experimental data is saved immediately using the current SI group saving options. If the close column values after acquisition option is enabled, the microscope column valves are closed (on systems that support column valve access). You can use the (still) active survey image on the View workspace to immediately restart an identical or similar acquisition after adjusting survey ROIs and parameters.